The strange thing is, that when I setup the ethernet part for the machine, the website seems to be automatically be available over ipv6.

If I do

lsof -i :443

i see that the Docker is automatic available to ipv6. But regarding to the actual Nginx config this makes no sense. I disabled IPv4 and can confirm that the website is also automatically available over IPv6.

That’s why I mentioned the site specific conf file in the same folder. Try putting the settings in that file and see if that works. I am pretty sure the site specific file isn’t re-written after every restart.